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oushujun / LTR_retriever

LTR_retriever is a highly accurate and sensitive program for identification of LTR retrotransposons; The LTR Assembly Index (LAI) is also included in this package.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5813529/
GNU General Public License v3.0
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The difference in LAI evaluated using the two methods is significant. #179

Open dongaoqian opened 3 weeks ago

dongaoqian commented 3 weeks ago

Hello, I evaluated the LAI using results from de novo LTR identification and EDTA, but the LAI values from the two results differ significantly. I would like to know which result I should trust and why there is such a large discrepancy.

In the example below, the LAI on top comes from the de novo LTR identification result (8.83), while the LAI below is from the EDTA result (19.16). These two values differ significantly. image

Here is my script： image

In the following script, ”sample_v20231009.fasta.mod.pass.list“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.raw/LTR/; ”sample_v20231009.fasta.mod.out“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.final/

image

oushujun commented 1 week ago

You should concatenate finder and harvest scn files and give it through —inharvest. LTR_Finder_parallel produces harvest format scn files by default.

Shujun

On Wed, Sep 18, 2024 at 8:18 AM dongaoqian @.***> wrote:

Hello, I evaluated the LAI using results from de novo LTR identification and EDTA, but the LAI values from the two results differ significantly. I would like to know which result I should trust and why there is such a large discrepancy.

In the example below, the LAI on top comes from the de novo LTR identification result (8.86), while the LAI below is from the EDTA result (19.16). These two values differ significantly. image.png (view on web) https://github.com/user-attachments/assets/a851c0de-a4fe-4c5d-bf37-50018a2b5448

Here is my script： image.png (view on web) https://github.com/user-attachments/assets/097fd4dc-618d-499e-b86d-05a40084ea55

In the following script, ”sample_v20231009.fasta.mod.pass.list“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.raw/LTR/; ”sample_v20231009.fasta.mod.out“ comes from ./run_EDTA/sample_v20231009.fasta.mod.EDTA.final/

image.png (view on web) https://github.com/user-attachments/assets/786f35da-c3fc-4d72-80e5-798496c04d26

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dongaoqian commented 2 days ago

Thank you for your reply. I reassessed the LAI using the first method, and the final result was 18.84, which differs by less than 1 from the LAI I evaluated using EDTA result.